Proton pump inhibitors induced fungal dysbiosis in patients with gastroesophageal reflux disease

Abstract

Gut mycobiota inhabits human gastrointestinal lumen and plays a role in human health and disease. We investigated the influence of proton pump inhibitors (PPIs) on gastric mucosal and fecal mycobiota in patients with gastroesophageal reflux diseases (GERD) by using Internal Transcribed Spacer 1 sequencing. A total of 65 participants were included, consisting of the healthy control (HC) group, GERD patients who did not use PPIs (nt-GERD), and GERD patients who used PPIs, which were further divided into short-term (s-PPI) and long-term PPI user (l-PPI) groups based on the duration of PPI use. The alpha diversity and beta diversity of gastric mucosal mycobiota in GERD patients with PPI use were significantly different from HCs, but there were no differences between s-PPI and l-PPI groups. LEfSe analysis identified Candida at the genus level as a biomarker for the s-PPI group when compared to the nt-GERD group. Meanwhile, Candida, Nothojafnea, Rhizodermea, Ambispora, and Saccharicola were more abundant in the l-PPI group than in the nt-GERD group. Furthermore, colonization of Candida in gastric mucosa was significantly increased after PPI treatment. However, there was no significant difference in Candida colonization between patients with endoscopic esophageal mucosal breaks and those without. There were significant differences in the fecal mycobiota composition between HCs and GERD patients regardless whether or not they used PPI. As compared to nt-GERD patient samples, there was a high abundance of Alternaria, Aspergillus, Mycenella, Exserohilum, and Clitopilus in the s-PPI group. In addition, there was a significantly higher abundance of Alternaria, Aspergillus, Podospora, Phallus, and Monographella in the l-PPI group than nt-GERD patients. In conclusion, our study indicates that dysbiosis of mycobiota was presented in GERD patients in both gastric mucosal and fecal mycobiota. PPI treatment may increase the colonization of Candida in the gastric mucosa in GERD patients.

Keywords: Candida; fecal mycobiota; gastric mucosal mycobiota; gastroesophageal reflux disease; proton pump inhibitor.

Figure 1

Stacked bar-plot representation of gastric mucosal mycobiota composition in nt-GERD, s-PPI, l-PPI, and HC with taxonomic features collapsed at the level of phyla and genera. (A) The composition of the fungi community at phylum levels among the groups. (B) The composition of the fungi community at genus levels among the groups. Only the top 20 taxa with the largest average relative abundance are listed.

Figure 2

Comparison of alpha diversities, including observed features (A) and Shannon index (B) among the four groups at gastric mucosal mycobiota. Comparison of beta diversities, including Bray–Curtis dissimilarity index (C) and weighted UniFrac distance (D) among the four groups by the PCoA at gastric fungal communities.

Figure 3

Linear discriminant analysis effect size (LEfSe) analysis of taxonomic features differentiating in gastric mucosal mycobiota between the nt-GERD group and the s-PPI group (A) and l-PPI group (B) (LDA values >2, p < 0.08) at the genus level. Differentially abundant taxa of each group are distinguished by different colors. Candida increased in patients treated with PPIs (C). At the genus level, the abundance of Candida in patients treated with PPIs (s-PPI and l-PPI group) was significantly higher than in the nt-GERD group and healthy controls (C).

Figure 4

Stacked bar-plot representation of fecal mycobiota composition in nt-GERD, s-PPI, l-PPI, and HC with taxonomic features collapsed at the level of phyla and genera. (A) The composition of the fungi community at phylum levels among the groups. (B) The composition of the fungi community at genus levels among the groups. Only the top 20 taxa with the largest average relative abundance are listed.

Figure 5

Comparison of alpha diversities, including observed features (A) and Shannon index (B) among the four groups at fecal mycobiota. Comparison of beta diversities, including Bray–Curtis dissimilarity index (C) and weighted UniFrac distance (D) among the four groups by the PCoA at fecal fungal communities.

Figure 6

Linear discriminant analysis effect size (LEfSe) analysis of taxonomic features differentiating in fecal mycobiota between the nt-GERD group and the s-PPI group (A) and l-PPI group (B) (LDA values >2, p < 0.08) at the genus level. Differentially abundant taxa of each group are distinguished by different colors.